[Genome] affymetrix

[Pauline Fujita]

Hello Yuan,

The data you are looking for is available in our table browser, which is 
found here:

http://www.genome.ucsc.edu/cgi-bin/hgTables

After selecting your assembly of interest select the "Expression and 
Regulation" group. The track you select will depend on which affymetrix 
array you are using. You can find out which arrays are available by 
looking at the pulldown list in the "track" menu of the table browser. 
If you click on "describe table schema" it will take you to a brief 
description of the table, and the contents of each column. You can also 
go to the genome browser for your assembly of interest and look at the 
tracks listed in the "Expression and Regulation" group. If you click on 
a track you can also see a description of the Affymetrix chip used.

Once you have determined which Affymetrix chip you are interested in - 
select this track (ie. Affy HuEx 1.0) and then select:

region: genome
output format: all fields from selected table.

then click on "get output". Note that if you only want probe set 
information for a region of the genome you can also specify this in the 
"region" line of the table browser by clicking position and entering 
your desired coordinates.

Hopefully this information was helpful and answers your question. If you 
have further questions or require clarification feel free to contact the 
mailing list at genome at soe.ucsc.edu.

Regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


Yuan Jian wrote:
> Hi UCSC genome,
>    
>   can I download affymetrix probeset infromation, such as chr strand.. from UCSC genome?
>    
>   thanks
>    
>   Yu
>    
>
>        
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